1. Operating System: Cygwin is not an operating system; it is a compatibility layer for running Linux applications on Windows. Fedora, on the other hand, is a full-fledged Linux operating system maintained by the community and sponsored by Red Hat.
2. Package Management: Cygwin uses its own package manager for installing and updating software packages, while Fedora relies on the DNF package manager for managing software installations and updates.
3. Default Desktop Environment: Fedora typically comes with the GNOME desktop environment as its default, providing a user-friendly graphical interface. Cygwin, as it runs on Windows, does not include a default desktop environment and primarily runs in a terminal window.
4. System Requirements: Fedora has specific system requirements for installation and runs on a variety of hardware configurations, while Cygwin can run on most Windows systems without stringent hardware requirements.
5. Community Support: Fedora has a large and active community of users and developers who provide support and updates for the operating system. Cygwin also has a community but is more focused on providing compatibility for running Linux tools on Windows rather than full operating system support.
6. Security: Fedora, being a Linux distribution, follows strict security guidelines and practices, while Cygwin, running on Windows, inherits the security features and vulnerabilities associated with the Windows environment.

In Summary, the key differences between Cygwin and Fedora lie in their nature as a compatibility layer versus an operating system, package management systems, default desktop environments, system requirements, community support, and security measures.